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Plot hole: Starship Avalon is supposed to be an extremely highly advanced spaceship with capabilities well beyond current technology. Because the pods are supposed to be "fail-safe"/fail-proof, no provisions whatsoever were made to detect a pod failure or sound an alarm - a severe "oversight" for the ingenious people/engineers behind its creation. There apparently are sensors everywhere to automatically activate certain things (e.g, doors, holograms) when a passenger or crew member enters or approaches yet some of the things the holograms said indicated they were preprogrammed to say certain things, even though those things weren't appropriate under the circumstances. For example, soon after Jim entered the room for Learning Group 38, a hologram said, "Hello, passengers. Will you all take a seat." Surely there would be a sensor to detect that all the passengers supposed to be present were or know that almost all were not! The holograms/androids could not respond to some anomalies.

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Other mistake: Near the end of the movie, three birds were flying around the room where trees, vines, flower, shrubs, and grass were growing. There is no explanation for where the birds came from, why Jim would revive them from pods (if that's where the first ones were), or why holograms wouldn't detect them. More seriously, where did all the bird droppings (guano) land - without being removed for decades - and how did the uric acid not cause damage/corrosion to the ship? Also, the confined area would be a breeding ground for various possible diseases which could infect the passengers when they came out of their pods. The unplanned introduction of live birds on the spaceship would cause a variety of unintended problems, some deadly.

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